Characterisation of a tripartite α-pore forming toxin from Serratia marcescens.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
19 03 2021
19 03 2021
Historique:
received:
02
10
2020
accepted:
03
03
2021
entrez:
20
3
2021
pubmed:
21
3
2021
medline:
21
3
2021
Statut:
epublish
Résumé
Tripartite members of the ClyA family of α-PFTs have recently been identified in a number of pathogenic Gram-negative bacteria, including the human pathogen Serratia marcescens. Structures of a Gram-negative A component and a tripartite α-PFT complete pore are unknown and a mechanism for pore formation is still uncertain. Here we characterise the tripartite SmhABC toxin from S. marcescens and propose a mechanism of pore assembly. We present the structure of soluble SmhA, as well as the soluble and pore forms of SmhB. We show that the β-tongue soluble structure is well conserved in the family and propose two conserved latches between the head and tail domains that are broken on the soluble to pore conformational change. Using the structures of individual components, sequence analysis and docking predictions we illustrate how the A, B and C protomers would assemble on the membrane to produce a complete tripartite α-PFT pore.
Identifiants
pubmed: 33742033
doi: 10.1038/s41598-021-85726-0
pii: 10.1038/s41598-021-85726-0
pmc: PMC7979752
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
6447Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/F016832/1
Pays : United Kingdom
Références
Yu, V. Serratia marcescens. N. Engl. J. Med. 46, 903–912 (1979).
Iguchi, A. et al. Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen. Genome Biol. Evol. 6, 2096–2110 (2014).
pubmed: 25070509
pmcid: 4231636
doi: 10.1093/gbe/evu160
Lacey, L. A. et al. Insect pathogens as biological control agents: back to the future. J. Invertebr. Pathol. 132, 1–41 (2015).
pubmed: 26225455
doi: 10.1016/j.jip.2015.07.009
Su, L. H. et al. Extended epidemic of nosocomial urinary tract infections caused by Serratia marcescens. J. Clin. Microbiol. 41, 4726–4732 (2003).
pubmed: 14532211
pmcid: 254321
doi: 10.1128/JCM.41.10.4726-4732.2003
Matilla, M. A., Udaondo, Z., Krell, T. & Salmond, G. P. C. Genome Sequence of Serratia marcescens MSU97, a plant-associated bacterium that makes multiple antibiotics. Genome Announc. 5, e01752-e1816 (2017).
pubmed: 28254993
pmcid: 5334600
doi: 10.1128/genomeA.01752-16
Anderson, M. T., Mitchell, L. A., Zhao, L. & Mobleya, H. L. T. Capsule production and glucose metabolism dictate fitness during Serratia marcescens bacteremia. MBio 8, e00740-e817 (2017).
pubmed: 28536292
pmcid: 5442460
doi: 10.1128/mBio.00740-17
Wilson, J. S. et al. Identification and structural analysis of the tripartite α-pore forming toxin of Aeromonas hydrophila. Nat. Commun. 10, 2900 (2019).
pubmed: 31263098
pmcid: 6602965
doi: 10.1038/s41467-019-10777-x
Fagerlund, A., Lindbäck, T., Storset, A. K., Granum, P. E. & Hardy, S. P. Bacillus cereus Nhe is a pore-forming toxin with structural and functional properties similar to the ClyA (HlyE, SheA) family of haemolysins, able to induce osmotic lysis in epithelia. Microbiology 154, 693–704 (2008).
pubmed: 18310016
doi: 10.1099/mic.0.2007/014134-0
Roderer, D. & Glockshuber, R. Assembly mechanism of the α-pore-forming toxin cytolysin A from Escherichia coli. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 372, 20160211 (2017).
pubmed: 28630151
pmcid: 5483514
doi: 10.1098/rstb.2016.0211
Eifler, N. et al. Cytotoxin ClyA from Escherichia coli assembles to a 13-meric pore independent of its redox-state. EMBO J. 25, 2652–2661 (2006).
pubmed: 16688219
pmcid: 1478193
doi: 10.1038/sj.emboj.7601130
Benke, S. et al. The assembly dynamics of the cytolytic pore toxin ClyA. Nat. Commun. 6, 6198 (2015).
pubmed: 25652783
doi: 10.1038/ncomms7198
Bräuning, B. et al. Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB. Nat. Commun. 9, 1806 (2018).
pubmed: 29728606
pmcid: 5935710
doi: 10.1038/s41467-018-04139-2
Schubert, E., Vetter, I. R., Prumbaum, D., Penczek, P. A. & Raunser, S. Membrane insertion of α-xenorhabdolysin in near-atomic detail. Elife 7, 1–25 (2018).
doi: 10.7554/eLife.38017
Sastalla, I. et al. The Bacillus cereus Hbl and Nhe tripartite enterotoxin components assemble sequentially on the surface of target cells and are not interchangeable. PLoS ONE 8, e76955 (2013).
pubmed: 24204713
pmcid: 3799921
doi: 10.1371/journal.pone.0076955
Beecher, D. J., Schoeni, J. L., Lee Wong, A. C. & Wong, A. C. Enterotoxic activity of hemolysin BL from Bacillus cereus. Infect. Immun. 63, 4423–4428 (1995).
pubmed: 7591080
pmcid: 173629
doi: 10.1128/iai.63.11.4423-4428.1995
Fox, D. et al. Bacillus cereus non-haemolytic enterotoxin activates the NLRP3 inflammasome. Nat. Commun. 11, 1–16 (2020).
doi: 10.1038/s41467-020-14534-3
Mathur, A. et al. A multicomponent toxin from Bacillus cereus incites inflammation and shapes host outcome via the NLRP3 inflammasome. Nat. Microbiol. 4, 362–374 (2019).
pubmed: 30531979
doi: 10.1038/s41564-018-0318-0
Tausch, F. et al. Evidence for complex formation of the Bacillus cereus haemolysin BL components in solution. Toxins (Basel) 9, 288 (2017).
doi: 10.3390/toxins9090288
Jessberger, N. et al. Binding to the target cell surface is the crucial step in pore formation of hemolysin BL from Bacillus cereus. Toxins (Basel) 11, 281 (2019).
doi: 10.3390/toxins11050281
Zhu, K. et al. Formation of small transmembrane pores: an intermediate stage on the way to Bacillus cereus non-hemolytic enterotoxin (Nhe) full pores in the absence of NheA. Biochem. Biophys. Res. Commun. 469, 613–618 (2016).
pubmed: 26654951
doi: 10.1016/j.bbrc.2015.11.126
Holm, L. & Laakso, L. M. Dali server update. Nucleic Acids Res. 44, 351–355 (2016).
doi: 10.1093/nar/gkw357
Wallace, A. J. et al. E. coli hemolysin E (HlyE, ClyA, SheA): X-ray crystal structure of the toxin and observation of membrane pores by electron microscopy. Cell 100, 265–276 (2000).
pubmed: 10660049
doi: 10.1016/S0092-8674(00)81564-0
Ganash, M. et al. Structure of the NheA component of the Nhe toxin from Bacillus cereus: implications for function. PLoS ONE 8, e74748 (2013).
pubmed: 24040335
pmcid: 3769298
doi: 10.1371/journal.pone.0074748
Didier, A., Dietrich, R. & Märtlbauer, E. Antibody binding studies reveal conformational flexibility of the Bacillus cereus non-hemolytic enterotoxin (Nhe) A-component. PLoS ONE 11, e0165135 (2016).
pubmed: 27768742
pmcid: 5074587
doi: 10.1371/journal.pone.0165135
Heilkenbrinker, U. et al. Complex formation between NheB and NheC is necessary to induce cytotoxic activity by the three-component Bacillus cereus Nhe enterotoxin. PLoS ONE 8, e63104 (2013).
pubmed: 23646182
pmcid: 3639968
doi: 10.1371/journal.pone.0063104
Madegowda, M., Eswaramoorthy, S., Burley, S. K. & Swaminathan, S. X-ray crystal structure of the B component of Hemolysin BL from Bacillus cereus. Proteins Struct. Funct. Genet. 71, 534–540 (2008).
pubmed: 18175317
doi: 10.1002/prot.21888
Dietrich, R., Moravek, M., Bürk, C., Granum, P. E. & Märtlbauer, E. Production and characterization of antibodies against each of the three subunits of the Bacillus cereus nonhemolytic enterotoxin complex. Appl. Environ. Microbiol. 71, 8214–8220 (2005).
pubmed: 16332805
pmcid: 1317347
doi: 10.1128/AEM.71.12.8214-8220.2005
Didier, A. et al. Monoclonal antibodies neutralize Bacillus cereus Nhe enterotoxin by inhibiting ordered binding of its three exoprotein components. Infect. Immun. 80, 832–838 (2012).
pubmed: 22104106
pmcid: 3264321
doi: 10.1128/IAI.05681-11
Van Zundert, G. C. P. et al. The HADDOCK2.2 web server: user-friendly integrative modeling of biomolecular complexes. J. Mol. Biol. 428, 720–725 (2016).
pubmed: 26410586
doi: 10.1016/j.jmb.2015.09.014
Churchill-Angus, A. M., Sedelnikova, S. E., Schofielda, T. H. B. & Baker, P. J. The A component (SmhA) of a tripartite pore-forming toxin from Serratia marcescens: expression, purification and crystallographic analysis. Acta Crystallogr. Sect. F Struct. Biol. Commun. 76, 577–582 (2020).
doi: 10.1107/S2053230X20013862
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
doi: 10.1016/S0022-2836(05)80360-2
pubmed: 2231712
Notredame, C., Higgins, D. G. & Heringa, J. T-coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217 (2000).
pubmed: 10964570
doi: 10.1006/jmbi.2000.4042
Rowe, G. E. & Welch, R. A. Assays of hemolytic toxins. Methods Enzymol. 235, 657–667 (1994).
pubmed: 7520121
doi: 10.1016/0076-6879(94)35179-1
Winter, G. et al. DIALS: Implementation and evaluation of a new integration package. Acta Crystallogr. Sect. D Struct. Biol. 74, 85–97 (2018).
doi: 10.1107/S2059798317017235
Winter, G. Xia2: An expert system for macromolecular crystallography data reduction. J. Appl. Crystallogr. 43, 186–190 (2010).
doi: 10.1107/S0021889809045701
Skubák, P. & Pannu, N. S. Automatic protein structure solution from weak X-ray data. Nat. Commun. 4, 2777 (2013).
pubmed: 24231803
doi: 10.1038/ncomms3777
Emsley, P. et al. Features and development of Coot. Acta Crystallogr. Sect. D 66, 486–501 (2010).
doi: 10.1107/S0907444910007493
Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997).
pubmed: 15299926
doi: 10.1107/S0907444996012255
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
pubmed: 19461840
pmcid: 2483472
doi: 10.1107/S0021889807021206
Vonrhein, C. et al. Data processing and analysis with the autoPROC toolbox. Acta Crystallogr. Sect. D Biol. Crystallogr. 67, 293–302 (2011).
doi: 10.1107/S0907444911007773
Kabsch, W. et al. XDS. Acta Crystallogr. Sect. D Biol. Crystallogr. 66, 125–132 (2010).
doi: 10.1107/S0907444909047337
Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution?. Acta Crystallogr. Sect. D Biol. Crystallogr. 69, 1204–1214 (2013).
doi: 10.1107/S0907444913000061
Winn, M. D. et al. Overview of the CCP 4 suite and current developments. Acta Crystallogr. Sect. D Biol. Crystallogr. 67, 235–242 (2011).
doi: 10.1107/S0907444910045749
Tickle, I. et al. STARANSIO (Global Phasing Ltd., 2019).
Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. E. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858 (2015).
pubmed: 25950237
pmcid: 5298202
doi: 10.1038/nprot.2015.053
Schrödinger, LLC. The {PyMOL} Molecular Graphics System, Version~1.8. (2015).